Impact of long-range attraction on desorption kinetics.

Desorption of molecules from surfaces is widespread both in nature and technology. Despite its omnipresence and conceptual simplicity, fundamental details can be surprisingly complex and are often poorly understood. In many cases, first-order kinetics is assumed, which implies that the adsorbates do not interact with each other and desorption is the rate-limiting process. While this might be a good approximation in some cases, it is far from reality in the case of adsorbates that form ordered structures. Here, we study the desorption of a submonolayer film of 3-nitrophenol from the natural cleavage plane of calcite kept in ultrahigh vacuum. Interestingly, two distinctly different desorption regimes are observed during isothermal desorption monitored by dynamic atomic force microscopy. Initially, at high coverages, the coverage decreases almost linearly in time, indicating a constant desorption rate. Beyond this linear regime, at low coverages, a drastic increase in desorption rate is observed until the surface is completely empty. The transition between these two regimes is associated with a critical island width. We propose an existence of a long-range attractive interaction between the molecules as a possible explanation for the sudden increase in the desorption rate when a critical island width is reached. The herein observed phenomenon of two different desorption regimes is expected to be of general nature when interactions beyond next-neighbour attraction are present.

Sumoylation of methionine adenosyltransferase alpha 1 promotes mitochondrial dysfunction in alcohol-associated liver disease.

BACKGROUND AND AIMS: Methionine adenosyltransferase alpha1 (MATα1) is responsible for the biosynthesis of S-adenosylmethionine in normal liver. Alcohol consumption enhances MATα1 interaction with peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1), which blocks MATα1 mitochondrial targeting, resulting in lower mitochondrial MATα1 content and mitochondrial dysfunction in alcohol-associated liver disease (ALD) in part through upregulation of cytochrome P450 2E1. Conversely, alcohol intake enhances SUMOylation, which enhances cytochrome P450 2E1 expression. MATα1 has potential SUMOylation sites, but whether MATα1 is regulated by SUMOylation in ALD is unknown. Here, we investigated if MATα1 is regulated by SUMOylation and, if so, how it impacts mitochondrial function in ALD. APPROACH AND RESULTS: Proteomics profiling revealed hyper-SUMOylation of MATα1, and prediction software identified lysine 48 (K48) as the potential SUMOylation site in mice (K47 in humans). Experiments with primary hepatocytes, mouse, and human livers revealed that SUMOylation of MAT1α by SUMO2 depleted mitochondrial MATα1. Furthermore, mutation of MATα1 K48 prevented ethanol-induced mitochondrial membrane depolarization, MATα1 depletion, and triglyceride accumulation. Additionally, CRISPR/CRISPR associated protein 9 gene editing of MATα1 at K48 hindered ethanol-induced MATα1-PIN1 interaction, degradation, and phosphorylation of MATα1 in vitro. In vivo, CRISPR/CRISPR associated protein 9 MATα1 K48 gene-edited mice were protected from ethanol-induced fat accumulation, liver injury, MATα1-PIN1 interaction, mitochondrial MATα1 depletion, mitochondrial dysfunction, and low S-adenosylmethionine levels. CONCLUSIONS: Taken together, our findings demonstrate an essential role for SUMOylation of MATα1 K48 for interaction with PIN1 in ALD. Preventing MATα1 K48 SUMOylation may represent a potential treatment strategy for ALD.

Ab Initio Electron-Phonon Interactions in Correlated Electron Systems.

Electron-phonon (e-ph) interactions are pervasive in condensed matter, governing phenomena such as transport, superconductivity, charge-density waves, polarons, and metal-insulator transitions. First-principles approaches enable accurate calculations of e-ph interactions in a wide range of solids. However, they remain an open challenge in correlated electron systems (CES), where density functional theory often fails to describe the ground state. Therefore reliable e-ph calculations remain out of reach for many transition metal oxides, high-temperature superconductors, Mott insulators, planetary materials, and multiferroics. Here we show first-principles calculations of e-ph interactions in CES, using the framework of Hubbard-corrected density functional theory (DFT+U) and its linear response extension (DFPT+U), which can describe the electronic structure and lattice dynamics of many CES. We showcase the accuracy of this approach for a prototypical Mott system, CoO, carrying out a detailed investigation of its e-ph interactions and electron spectral functions. While standard DFPT gives unphysically divergent and short-ranged e-ph interactions, DFPT+U is shown to remove the divergences and properly account for the long-range Fröhlich interaction, allowing us to model polaron effects in a Mott insulator. Our work establishes a broadly applicable and affordable approach for quantitative studies of e-ph interactions in CES, a novel theoretical tool to interpret experiments in this broad class of materials.

Fast Molecular Compression by a Hyperthermal Collision Gives Bond-Selective Mechanochemistry.

Using electrospray ion beam deposition, we collide the complex molecule Reichardt's dye (C_{41}H_{30}NO^{+}) at low, hyperthermal translational energy (2-50 eV) with a Cu(100) surface and image the outcome at single-molecule level by scanning tunneling microscopy. We observe bond-selective reaction induced by the translational kinetic energy. The collision impulse compresses the molecule and bends specific bonds, prompting them to react selectively. This dynamics drives the system to seek thermally inaccessible reactive pathways, since the compression timescale (subpicosecond) is much shorter than the thermalization timescale (nanosecond), thereby yielding reaction products that are unobtainable thermally.

Creating a regular array of metal-complexing molecules on an insulator surface at room temperature.

Controlling self-assembled nanostructures on bulk insulators at room temperature is crucial towards the fabrication of future molecular devices, e.g., in the field of nanoelectronics, catalysis and sensor applications. However, at temperatures realistic for operation anchoring individual molecules on electrically insulating support surfaces remains a big challenge. Here, we present the formation of an ordered array of single anchored molecules, dimolybdenum tetraacetate, on the (10.4) plane of calcite (CaCO3). Based on our combined study of atomic force microscopy measurements and density functional theory calculations, we show that the molecules neither diffuse nor rotate at room temperature. The strong anchoring is explained by electrostatic interaction of an ideally size-matched molecule. Especially at high coverage, a hard-sphere repulsion of the molecules and the confinement at the calcite surface drives the molecules to form locally ordered arrays, which is conceptually different from attractive linkers as used in metal-organic frameworks. Our work demonstrates that tailoring the molecule-surface interaction opens up the possibility for anchoring individual metal-complexing molecules into ordered arrays.

SUMOylation Protects FASN Against Proteasomal Degradation in Breast Cancer Cells Treated with Grape Leaf Extract.

Existing therapeutic strategies for breast cancer are limited by tumor recurrence and drug-resistance. Antioxidant plant-derived compounds such as flavonoids reduce adverse outcomes and have been identified as a potential source of antineoplastic agent with less undesirable side effects. Here, we describe the novel regulation of fatty-acid synthase (FASN), the key enzyme in de novo fatty-acid synthesis, whereby Vitis vinifera L. cv Vermentino leaf hydroalcoholic extract lowers its protein stability that is regulated by small ubiquitin-like modifier (SUMO)ylation. The phenolic compounds characterization was performed by liquid chromatography-mass spectrometry (LC-MS), whereas mass spectrometry (LC-MS/MS), Western blotting/co-immunoprecipitation (Co-IP) and RT-PCR, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), clonogenicity assays, and FACS analysis were used to measure the expression of targets and tumorigenicity. Vermentino extract exhibits antitumorigenic effects, and we went on to determine that FASN and ubiquitin-conjugating enzyme 9 (UBC9), the sole E2 enzyme required for SUMOylation, were significantly reduced. Moreover, FASN was found SUMOylated in human breast cancer tissues and cell lines, and lack of SUMOylation caused by SUMO2 silencing reduced FASN protein stability. These results suggest that SUMOylation protects FASN against proteasomal degradation and may exert oncogenic activity through alteration of lipid metabolism, whereas Vermentino extract inhibits these effects which supports the additional validation of the therapeutic value of this compound in breast cancer.

Controlling the preferential motion of chiral molecular walkers on a surface.

Molecular walkers standing on two or more "feet" on an anisotropic periodic potential of a crystal surface may perform a one-dimensional Brownian motion at the surface-vacuum interface along a particular direction in which their mobility is the largest. In thermal equilibrium the molecules move with equal probabilities both ways along this direction, as expected from the detailed balance principle, well-known in chemical reactivity and in the theory of molecular motors. For molecules that possess an asymmetric potential energy surface (PES), we propose a generic method based on the application of a time-periodic external stimulus that would enable the molecules to move preferentially in a single direction thereby acting as Brownian ratchets. To illustrate this method, we consider a prototypical synthetic chiral molecular walker, 1,3-bis(imidazol-1-ylmethyl)-5(1-phenylethyl)benzene, diffusing on the anisotropic Cu(110) surface along the Cu rows. As unveiled by our kinetic Monte Carlo simulations based on the rates calculated using ab initio density functional theory, this molecule moves to the nearest equivalent lattice site via the so-called inchworm mechanism in which it steps first with the rear foot and then with the front foot. As a result, the molecule diffuses via a two-step mechanism, and due to its inherent asymmetry, the corresponding PES is also spatially asymmetric. Taking advantage of this fact, we show how the external stimulus can be tuned to separate molecules of different chirality, orientation and conformation. The consequences of these findings for molecular machines and the separation of enantiomers are also discussed.

Correction: Controlling the preferential motion of chiral molecular walkers on a surface.

[This corrects the article DOI: 10.1039/C9SC01135H.].

Star-related lipid transfer protein 10 (STARD10): a novel key player in alcohol-induced breast cancer progression.

BACKGROUND: Ethanol abuse promotes breast cancer development, metastasis and recurrence stimulating mammary tumorigenesis by mechanisms that remain unclear. Normally, 35% of breast cancer is Erb-B2 Receptor Tyrosine Kinase 2 (ERBB2)-positive that predisposes to poor prognosis and relapse, while ethanol drinking leads to invasion of their ERBB2 positive cells triggering the phosphorylation status of mitogen-activated protein kinase. StAR-related lipid transfer protein 10 (STARD10) is a lipid transporter of phosphatidylcholine (PC) and phosphatidylethanolamine (PE); changes on membrane composition of PC and PE occur before the morphological tumorigenic events. Interestingly, STARD10 has been described to be highly expressed in 35-40% of ERBB2-positive breast cancers. In this study, we demonstrate that ethanol administration promotes STARD10 and ERBB2 expression that is significantly associated with increased cell malignancy and aggressiveness. MATERIAL AND METHODS: We investigated the effect of ethanol on STARD10-ERBB2 cross-talk in breast cancer cells, MMTV-neu transgenic mice and in clinical ERBB2-positive breast cancer specimens with Western Blotting and Real-time PCR. We also examined the effects of their knockdown and overexpression on transient transfected breast cancer cells using promoter activity, MTT, cell migration, calcium and membrane fluidity assays in vitro. RESULTS: Ethanol administration induces STARD10 and ERBB2 expression in vitro and in vivo. ERBB2 overexpression causes an increase in STARD10 expression, while overexpression of ERBB2's downstream targets, p65, c-MYC, c-FOS or c-JUN induces STARD10 promoter activity, correlative of enhanced ERBB2 function. Ethanol and STARD10-mediated cellular membrane fluidity and intracellular calcium concentration impact ERBB2 signaling pathway as evaluated by enhanced p65 nuclear translocation and binding to both ERBB2 and STARD10 promoters. CONCLUSION: Our finding proved that STARD10 and ERBB2 positively regulate each other's expression and function. Taken together, our data demonstrate that ethanol can modulate ERBB2's function in breast cancer via a novel interplay with STARD10.

On-surface synthesis on a bulk insulator surface.

On-surface synthesis has rapidly emerged as a most promising approach to prepare functional molecular structures directly on a support surface. Compared to solution synthesis, performing chemical reactions on a surface offers several exciting new options: due to the absence of a solvent, reactions can be envisioned that are otherwise not feasible due to the insolubility of the reaction product. Perhaps even more important, the confinement to a two-dimensional surface might enable reaction pathways that are not accessible otherwise. Consequently, on-surface synthesis has attracted great attention in the last decade, with an impressive number of classical reactions transferred to a surface as well as new reactions demonstrated that have no classical analogue. So far, the majority of the work has been carried out on conducting surfaces. However, when aiming for electronic decoupling of the resulting structures, e.g. for the use in future molecular electronic devices, non-conducting surfaces are highly desired. Here, we review the current status of on-surface reactions demonstrated on the (10.4) surface of the bulk insulator calcite. Besides thermally induced C-C coupling of halogen-substituted aryls, photochemically induced [2 + 2] cycloaddition has been proven possible on this surface. Moreover, experimental evidence exists for coupling of terminal alkynes as well as diacetylene polymerization. While imaging of the resulting structures with dynamic atomic force microscopy provides a direct means of reaction verification, the detailed reaction pathway often remains unclear. Especially in cases where the presence of metal atoms is known to catalyze the corresponding solution chemistry reaction (e.g. in the case of the Ullmann reaction), disclosing the precise reaction pathway is of importance to understand and generalize on-surface reactivity on a bulk insulator surface. To this end, density-functional theory calculations have proven to provide atomic-scale insights that have greatly contributed to unravelling the details of on-surface synthesis on a bulk insulator surface.

SUMOylation regulates cytochrome P450 2E1 expression and activity in alcoholic liver disease.

Alcohol acts through numerous pathways leading to alcoholic liver disease (ALD). Cytochrome P450 (CYP2E1), an ethanol-inducible enzyme, metabolizes ethanol-producing toxic reactive oxygen species (ROS) and is regulated at the posttranslational level. Small ubiquitin-like modifier (SUMO)ylation is a posttranslational modification that involves the addition of SUMOs, which modulate protein stability, activity, and localization. We demonstrated that ubiquitin-conjugation enzyme 9, the SUMO-conjugating enzyme, is induced in the livers of an intragastric ethanol mouse model. Our aim is to examine whether SUMOylation could regulate ethanol-induced CYP2E1 expression in ALD and to elucidate the molecular mechanism(s). CYP2E1 and UBC9 expression in vitro and in vivo was detected by real-time PCR and immunoblotting/immunostaining. SUMOylation was assayed by mass spectrometry and coimmunoprecipitation. Ubc9 expression was induced in ethanol-fed mouse livers, and silencing inhibited ethanol-mediated CYP2E1 microsomal retention and enzymatic activity. CYP2E1 SUMOylation was found to be induced by ethanol in vitro and in vivo. Ubc9 silencing prevents ethanol-induced lipid accumulation and ROS production. UBC9 was highly expressed in human ALD livers. Finally, we found that lysine 410 is a key SUMOylated residue contributing to CYP2E1 protein stability and activity preventing CYP2E1 SUMOylation. Ethanol-mediated up-regulation of CYP2E1 via SUMOylation enhancing its protein stability and activity and may have important implications in ALD.-Tomasi, M. L., Ramani, K., Ryoo, M., Cossu, C., Floris, A., Murray, B. J., Iglesias-Ara, A., Spissu, Y., Mavila, N. SUMOylation regulates cytochrome P450 2E1 expression and activity in alcoholic liver disease.

S-adenosylmethionine and methylthioadenosine inhibit cancer metastasis by targeting microRNA 34a/b-methionine adenosyltransferase 2A/2B axis.

MicroRNA-34a (miR-34a) is down-regulated in colorectal cancers (CRC) and required for interleukin-6 (IL-6)-induced CRC metastasis. Mice lacking miR-34a developed more invasive cancer in a colitis-associated cancer model. In the same model, S-adenosylmethionine (SAMe) and methylthioadenosine (MTA) inhibited IL-6/STAT3 and lowered tumor burden. SAMe and MTA reduce the expression of methionine adenosyltransferase 2A (MAT2A) and there are consensus binding sites for miR-34a/b in the MAT2A 3'UTR. Here we examined whether SAMe/MTA influence miR-34a/b expression and cancer metastasis. We found SAMe and MTA raised miR-34a/b expression in CRC cell lines, inhibited migration and invasion in vitro and liver metastasis in vivo. Like CRC, MAT2A and MAT2B expression is induced in human pancreas and prostate cancers. Treatment with SAMe, MTA, miR-34a or miR-34b inhibited MAT2A expression mainly at the protein level. MAT2B protein level also fell because MAT2A and MAT2B enhance each other's protein stability. Overexpressing miR-34a or miR-34b inhibited while MAT2A or MAT2B enhanced CRC migration and invasion. Co-expressing either miR-34a/b had minimal to no effect on MAT2A/MAT2B's ability to increase migration, invasion and growth. Taken together, MAT2A and MAT2B are important targets of miR-34a/b and SAMe and MTA target this axis, suppressing MAT2A/MAT2B while raising miR-34a/b expression, inhibiting cancer metastasis.

Driving Forces for Covalent Assembly of Porphyrins by Selective C-H Bond Activation and Intermolecular Coupling on a Copper Surface.

Recent synthesis of covalent organic assemblies at surfaces has opened the promise of producing robust nanostructures for functional interfaces. To uncover how this new chemistry works at surfaces and understand the underlying mechanisms that control bond-breaking and bond-making processes at specific positions of the participating molecules, we study here the coupling reaction of tetra(mesityl)porphyrin molecules, which creates covalently connected networks on the Cu(110) surface by utilizing the 4-methyl groups as unique connection points. Using scanning tunneling microscopy (STM), state-of-the-art density functional theory (DFT), and Nudged Elastic Band (NEB) calculations, we show that the unique directionality of the covalent bonding is found to stem from a chain of highly selective C-H activation and dehydrogenation processes, followed by specific intermolecular C-C coupling reactions that are facilitated by the surface, by steric constraints, and by anisotropic molecular diffusion. These insights provide the first steps toward developing synthetic rules for complex two-dimensional covalent organic chemistry that can be enacted directly at a surface to deliver specific macromolecular structures designed for specific functions.

Reduced stress granule formation and cell death in fibroblasts with the A382T mutation of TARDBP gene: evidence for loss of TDP-43 nuclear function.

TAR deoxyribonucleic acid-binding protein 43 (TDP-43) is a key protein in the pathogenesis of amyoptrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Recent studies suggest that mutations in the TDP-43 coding gene, TARDBP, as well as variations in TDP-43 protein expression levels may disrupt the dynamics of stress granules (SGs). However, it remains unclear whether the pathogenetic effect of the TDP-43 protein is exerted at the cytoplasmic level, through direct participation to SG composition, or at nuclear level, through control of proteins essential to SG assembly. To clarify this point, we investigated the dynamics of SG formation in primary skin fibroblast cultures from the patients with ALS together with the A382T mutation and the patients with ALS and healthy controls with wild-type TDP-43. Under stress conditions induced by sodium arsenite, we found that in human fibroblasts TDP-43 did not translocate to the SGs but instead contributed to the SG formation through a regulatory effect on the G3BP1 core protein. We found that the A382T mutation caused a significant reduction in the number of SGs per cell (P < 0.01) as well as the percentage of cells that form SGs (P < 0.00001). Following stress stimuli, a significant decrease of viability was observed for cells with the TDP-43 A382T mutation (P < 0.0005). We can therefore conclude that the A382T mutation caused a reduction in the ability of cells to respond to stress through loss of TDP-43 function in SG nucleation. The pathogenetic action revealed in our study model does not seem to be mediated by changes in the localization of the TDP-43 protein.

A small molecule walks along a surface between porphyrin fences that are assembled in†situ.

An on-surface bimolecular system is described, comprising a simple divalent bis(imidazolyl) molecule that is shown to "walk" at room temperature via an inchworm mechanism along a specific pathway terminated at each end by oligomeric "fences" constructed on a monocrystalline copper surface. Scanning tunneling microscopy shows that the motion of the walker occurs along the [110] direction of the Cu surface with remarkably high selectivity and is effectively confined by the orthogonal construction of covalent porphyrin oligomers along the [001] surface direction, which serve as barriers. Density functional theory shows that the mobile molecule walks by attaching and detaching the nitrogen atoms in its imidazolyl "legs" to and from the protruding close-packed rows of the metal surface and that it can transit between two energetically equivalent extended and contracted conformations by overcoming a small energy barrier.

Anomalous coarsening driven by reversible charge transfer at metal-organic interfaces.

The unique electronic properties and functional tunability of polycyclic aromatic hydrocarbons have recently fostered high hopes for their use in flexible, green, portable, and cheap technologies. Most applications require the deposition of thin molecular films onto conductive electrodes. The growth of the first few molecular layers represents a crucial step in the device fabrication since it determines the structure of the molecular film and the energy level alignment of the metal-organic interface. Here, we explore the formation of this interface by analyzing the interplay between reversible molecule-substrate charge transfer, yielding intermolecular repulsion, and van der Waals attractions in driving the molecular assembly. Using a series of ad hoc designed molecules to balance the two effects, we combine scanning tunnelling microscopy with atomistic simulations to study the self-assembly behavior. Our systematic analysis identifies a growth mode characterized by anomalous coarsening that we anticipate to occur in a wide class of metal-organic interfaces and which should thus be considered as integral part of the self-assembly process when depositing a molecule on a conducting surface.

Fine-tuning the electrostatic properties of an alkali-linked organic adlayer on a metal substrate.

The performance of modern organic electronic devices is often determined by the electronic level alignment at a metal-organic interface. This property can be controlled by introducing an interfacial electrostatic dipole via the insertion of a stable interlayer between the metallic and the organic phases. Here, we use density functional theory to investigate the electrostatic properties of an assembled structure formed by alkali metals coadsorbed with 7,7,8,8-tetracyanoquinodimethane (TCNQ) molecules on a Ag(100) substrate. We find that the interfacial dipole buildup is regulated by the interplay of adsorption energetics, steric constraints and charge transfer effects, so that choosing chemical substitutions within TCNQ and different alkali metals provides a rich playground to control the systems' electrostatics and in particular fine-tune its work-function shift.

Absence of activating killer immunoglobulin-like receptor genes combined with hepatitis C viral genotype is predictive of hepatocellular carcinoma.

Killer immunoglobulin-like receptors and their human leukocyte antigen class I ligands have a critical role in natural killer cell response to viral pathogens and tumors. To investigate whether killer immunoglobulin-like receptor genes could influence the chronic course of hepatitis C virus infection and/or progression to hepatocellular carcinoma we retrospectively analyzed a cohort of 228 patients transplanted for hepatitis C virus-induced cirrhotic end stage liver disease, combined or not with hepatocellular carcinoma. We found that patients completely lacking activating killer immunoglobulin-like receptor genes had a high risk of developing hepatocellular carcinoma. Hepatitis C viral genotype and viral load are other risk factors that can influence the course of chronic hepatitis C virus infection. In our study, the risk conferred by hepatitis C viral genotypes was enhanced in patients lacking activating killer immunoglobulin-like receptors. These results point to an important role for activating killer immunoglobulin-like receptors in the control of hepatitis C virus infection and progression to hepatocellular carcinoma. In clinical practice, assessment of killer immunoglobulin-like receptor and hepatitis C viral genotype combinations should allow for more accurate monitoring of patients with chronic hepatitis C virus infection.

Homozygosity for killer immunoglobin-like receptor haplotype A predicts complete molecular response to treatment with tyrosine kinase inhibitors in chronic myeloid leukemia patients.

Several recent reports suggest a possible role for killer immunoglobulin-like receptors (KIR) in the onset of chronic myeloid leukemia (CML) and response to therapy with tyrosine kinase inhibitors (TKIs). To explore this hypothesis, we studied KIRs and their human leukocyte antigen class I ligands in 59 consecutive patients with chronic-phase CML (mean age, 53 years; range, 23-81 years) and a group of 121 healthy control participants belonging to the same ethnic group as the patients. The 2-year cumulative incidence of complete molecular response, obtained after a median of 27 months (range, 4-52 months), was 51.2%. An increased frequency of the activating receptor KIR2DS1 (pm = 0.05) and a reduced frequency of the KIR-ligand combination KIR2DS2/2DL2 absent/C1 present (pm = 0.001) were significantly associated with CML. Moreover, KIR repertoires in patients appeared to influence response to TKI therapy. Homozygosity for KIR haplotype A (pm = 0.01), a decreased frequency of the inhibitory KIR gene KIR2DL2 (pm = 0.02), and low numbers of inhibitory KIR genes (pm = 0.05) were all significantly associated with achievement of complete molecular remission. These data suggest that a decrease in properly stimulated and activated NK cells might contribute to the occurrence of CML and indicate homozygosity for KIR haplotype A as a promising immunogenetic marker of complete molecular response that could help clinicians decide whether to withdraw treatment in patients with CML.